Question: Unable to annotate in ChIPQC using yeast genome
0
gravatar for bertb
10 days ago by
bertb0
bertb0 wrote:

Hello,

I am trying to do a ChIPQC analysis, but it appears that annotations for Saccharomyces Cerevisiae are not supported:


> library(ChIPQC)
> samples = read.csv("sample.sheet.csv")
> CQCanalysis = ChIPQC(samples, annotation="sacCer3")
swn1   WT none 1 macs
swn2   WT none 2 macs
swh1   WT hs 1 macs
swh2   WT hs 2 macs
smn1   MT none 1 macs
smn2   MT none 2 macs
smh1   MT hs 1 macs
smh2   MT hs 2 macs
Checking chromosomes:
[1] "chrI"
Compiling annotation...
Error in getAnnotation(annotation, AllChr = chromosomes) : 
  Unsupported annotation:sacCer3

After reading a bit further, I understand you can create a custom gene annotation, so I tried the following:


> library(TxDb.Scerevisiae.UCSC.sacCer3.sgdGene)
> library(GenomicRanges)
> library(ChIPpeakAnno)
> yGR <- toGRanges(TxDb.Scerevisiae.UCSC.sacCer3.sgdGene)
> yGR
GRanges object with 6534 ranges and 0 metadata columns:
            seqnames        ranges strand
               <Rle>     <IRanges>  <Rle>
      Q0010     chrM     3952-4415      +
      Q0032     chrM   11667-11957      +
      Q0055     chrM   13818-26701      +
      Q0075     chrM   24156-25255      +
      Q0080     chrM   27666-27812      +
        ...      ...           ...    ...
    YPR200C   chrXVI 939279-939671      -
    YPR201W   chrXVI 939922-941136      +
    YPR202W   chrXVI 943032-944188      +
  YPR204C-A   chrXVI 946856-947338      -
    YPR204W   chrXVI 944603-947701      +
  -------
  seqinfo: 17 sequences (1 circular) from sacCer3 genome

> customAnno <- list(version="sacCer3", Test=yGR)
> CQCanalysis = ChIPQC(samples, annotation="customAnno")
swn1   WT none 1 macs
swn2   WT none 2 macs
swh1   WT hs 1 macs
swh2   WT hs 2 macs
smn1   MT none 1 macs
smn2   MT none 2 macs
smh1   MT hs 1 macs
smh2   MT hs 2 macs
Checking chromosomes:
[1] "chrI"
Compiling annotation...
Error in getAnnotation(annotation, AllChr = chromosomes) : 
  Unsupported annotation:customAnno

Any advice would be appreciated,

Thanks,

Ben

> sessionInfo()
R version 3.6.0 (2019-04-26)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17134)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
 [1] grid      parallel  stats4    stats     graphics  grDevices utils     datasets  methods  
[10] base     

other attached packages:
 [1] ChIPpeakAnno_3.18.0                         VennDiagram_1.6.20                         
 [3] futile.logger_1.4.3                         Biostrings_2.52.0                          
 [5] XVector_0.24.0                              TxDb.Scerevisiae.UCSC.sacCer3.sgdGene_3.2.2
 [7] GenomicFeatures_1.36.0                      AnnotationDbi_1.46.0                       
 [9] ChIPQC_1.20.0                               DiffBind_2.12.0                            
[11] SummarizedExperiment_1.14.0                 DelayedArray_0.10.0                        
[13] BiocParallel_1.17.18                        matrixStats_0.54.0                         
[15] Biobase_2.44.0                              GenomicRanges_1.36.0                       
[17] GenomeInfoDb_1.20.0                         IRanges_2.18.0                             
[19] S4Vectors_0.22.0                            BiocGenerics_0.30.0                        
[21] ggplot2_3.1.1                              

loaded via a namespace (and not attached):
  [1] amap_0.8-16                               colorspace_1.4-1                         
  [3] seqinr_3.4-5                              rjson_0.2.20                             
  [5] hwriter_1.3.2                             ggrepel_0.8.1                            
  [7] bit64_0.9-7                               splines_3.6.0                            
  [9] TxDb.Rnorvegicus.UCSC.rn4.ensGene_3.2.2   ade4_1.7-13                              
 [11] Nozzle.R1_1.1-1                           Rsamtools_2.0.0                          
 [13] annotate_1.62.0                           GO.db_3.8.2                              
 [15] pheatmap_1.0.12                           graph_1.62.0                             
 [17] TxDb.Hsapiens.UCSC.hg18.knownGene_3.2.2   BiocManager_1.30.4                       
 [19] compiler_3.6.0                            httr_1.4.0                               
 [21] GOstats_2.50.0                            backports_1.1.4                          
 [23] assertthat_0.2.1                          Matrix_1.2-17                            
 [25] lazyeval_0.2.2                            TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2  
 [27] limma_3.40.0                              formatR_1.6                              
 [29] prettyunits_1.0.2                         tools_3.6.0                              
 [31] gtable_0.3.0                              glue_1.3.1                               
 [33] GenomeInfoDbData_1.2.1                    Category_2.50.0                          
 [35] reshape2_1.4.3                            systemPipeR_1.18.0                       
 [37] dplyr_0.8.0.1                             batchtools_0.9.11                        
 [39] rappdirs_0.3.1                            ShortRead_1.42.0                         
 [41] Rcpp_1.0.1                                TxDb.Dmelanogaster.UCSC.dm3.ensGene_3.2.2
 [43] TxDb.Mmusculus.UCSC.mm9.knownGene_3.2.2   multtest_2.40.0                          
 [45] gdata_2.18.0                              rtracklayer_1.44.0                       
 [47] TxDb.Mmusculus.UCSC.mm10.knownGene_3.4.7  stringr_1.4.0                            
 [49] ensembldb_2.8.0                           gtools_3.8.1                             
 [51] XML_3.98-1.19                             idr_1.2                                  
 [53] edgeR_3.26.1                              MASS_7.3-51.4                            
 [55] zlibbioc_1.30.0                           scales_1.0.0                             
 [57] BSgenome_1.52.0                           VariantAnnotation_1.30.0                 
 [59] ProtGenerics_1.16.0                       hms_0.4.2                                
 [61] RBGL_1.60.0                               AnnotationFilter_1.8.0                   
 [63] lambda.r_1.2.3                            RColorBrewer_1.1-2                       
 [65] curl_3.3                                  yaml_2.2.0                               
 [67] memoise_1.1.0                             biomaRt_2.40.0                           
 [69] latticeExtra_0.6-28                       stringi_1.4.3                            
 [71] RSQLite_2.1.1                             genefilter_1.66.0                        
 [73] checkmate_1.9.3                           caTools_1.17.1.2                         
 [75] chipseq_1.34.0                            rlang_0.3.4                              
 [77] pkgconfig_2.0.2                           bitops_1.0-6                             
 [79] TxDb.Celegans.UCSC.ce6.ensGene_3.2.2      lattice_0.20-38                          
 [81] purrr_0.3.2                               GenomicAlignments_1.20.0                 
 [83] bit_1.1-14                                tidyselect_0.2.5                         
 [85] GSEABase_1.46.0                           AnnotationForge_1.26.0                   
 [87] plyr_1.8.4                                magrittr_1.5                             
 [89] R6_2.4.0                                  gplots_3.0.1.1                           
 [91] base64url_1.4                             DBI_1.0.0                                
 [93] pillar_1.4.0                              withr_2.1.2                              
 [95] survival_2.44-1.1                         RCurl_1.95-4.12                          
 [97] tibble_2.1.1                              crayon_1.3.4                             
 [99] futile.options_1.0.1                      KernSmooth_2.23-15                       
[101] progress_1.2.1                            locfit_1.5-9.1                           
[103] data.table_1.12.2                         blob_1.1.1                               
[105] Rgraphviz_2.28.0                          digest_0.6.18                            
[107] xtable_1.8-4                              regioneR_1.16.1                          
[109] brew_1.0-6                                munsell_0.5.0 

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